VAST Search Help

VAST Search is a WWW service which allows you to compare the 3-dimensional structure of an input protein with other protein structures in NCBI's MMDB, using the VAST algorithm.

The submitted file should be in plain-text (Ascii) in PDB format. (Important: Word documents will not work!!!) The file only needs to contain ATOM records for chain(s), and HETATM records for any heterogens. It does not need any SEQRES records or others that do not contain atomic coordinates. Click here for an example input file.

To submit a file to VAST Search, on the VAST Search home page enter the full path name of the file in the text box to the right of the [Submit] button, or use the [Browse] button to select your file. Then click on the [Submit] button to begin. This step will convert the PDB-format file into the Asn1-format file that is used for the VAST Search.

How to select a database search set?

You have the option of performing the search against a database consisting of a non-redundant subset of the PDB, or all of PDB. The non-redundant subset was selected by clustering the protein sequences at a BLAST P-value cutoff of 10e-40. The resulting set of representatives is about 1/10-th the size of the full database, and the search time should be proportionally faster.

Where to see the 3D structure of your protein and how to launch a VAST Search job?

After the input file is processed you will be taken to the structure summary page and informed "Data Parsing Done". Your Request Id is displayed; copy and save it, you will need it to see the final results!

The structure summary of your query is displayed in a table and in graphics as well. The graphic "rulers" corresponding to the chains in your input file. If there are protein chains and 3D domains are present, then these domains will also be displayed with graphics, where you can see the locations and boundaries of each 3D domain on the protein chain.

You can also use the [View 3D Structure] button to verify that your file has been input correctly. The option "Display" will display the structure using the Cn3D graphics viewer. The options "See File" or "Save File" allow you to directly view the ASN1-format file, or to save it to your local disk. If you are satisfied that your file has been converted correctly, then click on the [Start] button to begin the actual VAST Search. This will take you to the status monitoring page to tell you that the "Search in Progress" and inform you the results of your search job timely.

How long may it take to complete a VAST Search job?

There are 3 main factors that will influence the running time of VAST Search. First, if you choose to search the non-redundant subset (which is recommended), then the search will run about 10 times faster than for searching the entire database. Second, if you have multiple protein chains in your file, or large chains that split into many domains, then this will also lengthen the time to complete the search. Third, the type of the fold will also have an influence. A VAST Search with a structure such as a TIM barrel, for which there are very many other TIM barrels in the database (even the non-redundant one), will take much longer than a search with a fold that is less populated in the database.

How to view results of VAST Search?

The status monitoring page will take you to the result summary page automatically after a search job has completed. Or on the VAST Search home page enter your Request Id in the box adjacent to the [Show] button. Then click on [Show]. If the VAST Search job has not yet completed, then you will be informed of the status; if it has, then you will see the result summary page which tell you that "Search Job Completed".

The summary information will be detailed in a summary table. Besides the structure summary about the query chains/domain, the table describes how many structures in the database search set you chose when you sumbmitted your file are significantly similar to the query chain/domain, as found by VAST. Follow the links in the table, you will see the detailed footprints of alignments between each query chain/domain and their neighbors. Important: Since VAST returns neighbors that are deemed significant according to it's E-value, and this E-value is related to the size of the structure, it is not unusual for the neighbor lists for the entire chain and the domains to be different.

If you forget what your protein looks like and want to view its 3D structure, you may click on the [View] button of "View the Summary (graphical)" on the summary page. Besides viewing the structure in the graphics, you may click on the ruler for an entire chain to see the VAST structure neighbors for that entire chain; click on the bars for the domains to see the VAST structure neighbors for those domains.

Where to see individual VAST structure neighbor?

The VAST structure neighbors are introduced to you by clicking links in the VAST Search result summary page. All neighbors are given their names and alignment footprints in the graphics on the neighboring page. Besides, the page has several options available for viewing the alignments, selecting a subset to display, sorting neighbors based on various measures and looking for possible structure similar candidates:

[View 3D Structure]: This button can be used to view structural superpositions in Cn3D, or to output the superpositions into a file. Select the neighbors you wish to view by clicking the checkboxes to the left of the PDB codes in the neighbor list. Up to 10 neighbors may be selected. If you wish to See or Save the file, see the options under "Display".
[View Alignment]: This may be used to obtain a text version of the sequence alignments corresponding to the structural superposition of selected (check-boxed) neighbors.
[List]: for selecting subsets, sorting by alignment quantities such as alignment length, root mean square deviation, percent identical residues, etc.
[Find]: for selecting or looking for neighbors by PDB/MMDB/or domain identifiers.

For more information please see VAST Help

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